Repair Foci as Liquid Phase Separation: Evidence and Limitations
Abstract
:1. Introduction on DNA Repair of Double Strand Break
1.1. Mechanisms of DSB Repair
1.2. Repair Condensates Are Formed in Response to DNA Repair
2. Models of Condensates
2.1. Different Models of Membrane-Less Sub-Compartments
2.2. Criteria to Define PPPS and LLPS
2.2.1. “Standard Criteria” in the Literature to Demonstrate That a Condensate Forms via LLPS
Maintenance of a Spherical Shape
Wetting Behavior
Fuse after Touching
Mobility of the Molecules within the Condensate
2.2.2. Evolving Metrics for LLPS
Concentration Dependence
Internal Mixing
Diffusion across Boundary
Type of Motion within the Condensate
Diffusivity/Concentration Relation and Free Energy
2.2.3. Additional Macroscopic Criteria
Formation of Droplets In Vitro
Dissolution upon the 1.6-Hexanediol
Change in Light Diffraction Observed by Transmission
3. Evidence and Limitations of Liquid Phase Separation at DNA Repair Sites
3.1. Technical Limitations
3.2. Evidence of Liquid Phase Separation at DNA Repair Sites
3.2.1. PAR Chains, FUS, EWS and TAF15
3.2.2. 53BP1 and p53
3.2.3. Rad52 Proteins in Yeast
3.2.4. SSB in E. coli
3.3. Limitation of the LLPS Model in the Context of DSB Repair
3.3.1. RPA Foci Do Not Exhibit LLPS Properties in Yeast
3.3.2. Rad51 Forms Foci and Filaments at DSB Sites, Inconsistent with LLPS
3.3.3. Internal Architecture of Repair Foci
4. The Origin of Phase Separation and Their Possible Functions
4.1. Origin of Phase Separation
4.1.1. Liquid Phase Separation by RNA during DNA Repair
4.1.2. Liquid Phase Separation by Poly(ADP-Ribose)
4.1.3. Liquid Phase Separation by Repair Proteins
4.2. Possible Functions of Liquid Phase Separation
4.2.1. Efficiently Create Micro-Environments with High Local Concentration of Specific Proteins
4.2.2. Buffer the Concentration of Proteins
4.2.3. Reshape Chromatin at Damage Sites
4.2.4. LLPS in the Origin of Life
5. Conclusions
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
- Lindahl, T.; Barnes, D.E. Repair of Endogenous DNA Damage. Cold Spring Harb. Symp. Quant. Biol. 2000, 65, 127–134. [Google Scholar] [CrossRef] [PubMed]
- Vilenchik, M.M.; Knudson, A.G. Endogenous DNA double-strand breaks: Production, fidelity of repair, and induction of cancer. Proc. Natl. Acad. Sci. USA 2003, 100, 12871–12876. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Pastink, A.; Eeken, J.C.J.; Lohman, P.H.M. Genomic integrity and the repair of double-strand DNA breaks. Mutat. Res. Fundam. Mol. Mech. Mutagen. 2001, 480–481, 37–50. [Google Scholar] [CrossRef]
- Iliakis, G.; Wang, H.; Perrault, A.R.; Boecker, W.; Rosidi, B.; Windhofer, F.; Wu, W.; Guan, J.; Terzoudi, G.; Pantelias, G. Mechanisms of DNA double strand break repair and chromosome aberration formation. Cytogenet. Genome Res. 2004, 104, 14–20. [Google Scholar] [CrossRef] [PubMed]
- Mao, Z.; Bozzella, M.; Seluanov, A.; Gorbunova, V. Comparison of nonhomologous end joining and homologous recombination in human cells. DNA Repair 2008, 7, 1765–1771. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Liu, C.; Vyas, A.; Kassab, M.A.; Singh, A.K.; Yu, X. The role of poly ADP-ribosylation in the first wave of DNA damage response. Nucleic Acids Res. 2017, 45, 8129–8141. [Google Scholar] [CrossRef] [PubMed]
- Haince, J.-F.; McDonald, D.; Rodrigue, A.; Déry, U.; Masson, J.-Y.; Hendzel, M.J.; Poirier, G.G. PARP1-dependent Kinetics of Recruitment of MRE11 and NBS1 Proteins to Multiple DNA Damage Sites. J. Biol. Chem. 2008, 283, 1197–1208. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Ludwig, A.; Behnke, B.; Holtlund, J.; Hilz, H. Immunoquantitation and size determination of intrinsic poly(ADP-ribose) polymerase from acid precipitates. An analysis of the in vivo status in mammalian species and in lower eukaryotes. J. Biol. Chem. 1988, 263, 6993–6999. [Google Scholar] [CrossRef]
- Ali, A.A.E.; Timinszky, G.; Arribas-Bosacoma, R.; Kozlowski, M.; Hassa, P.O.; Hassler, M.; Ladurner, A.G.; Pearl, L.H.; Oliver, A.W. The zinc-finger domains of PARP1 cooperate to recognize DNA strand breaks. Nat. Struct. Mol. Biol. 2012, 19, 685–692. [Google Scholar] [CrossRef] [Green Version]
- Jungmichel, S.; Rosenthal, F.; Altmeyer, M.; Lukas, J.; Hottiger, M.O.; Nielsen, M.L. Proteome-wide Identification of Poly(ADP-Ribosyl)ation Targets in Different Genotoxic Stress Responses. Mol. Cell 2013, 52, 272–285. [Google Scholar] [CrossRef] [PubMed]
- Sellou, H.; Lebeaupin, T.; Chapuis, C.; Smith, R.; Hegele, A.; Singh, H.R.; Kozlowski, M.; Bultmann, S.; Ladurner, A.G.; Timinszky, G.; et al. The poly(ADP-ribose)-dependent chromatin remodeler Alc1 induces local chromatin relaxation upon DNA damage. MBoC 2016, 27, 3791–3799. [Google Scholar] [CrossRef]
- Izhar, L.; Adamson, B.; Ciccia, A.; Lewis, J.; Pontano-Vaites, L.; Leng, Y.; Liang, A.C.; Westbrook, T.F.; Harper, J.W.; Elledge, S.J. A Systematic Analysis of Factors Localized to Damaged Chromatin Reveals PARP-Dependent Recruitment of Transcription Factors. Cell Rep. 2015, 11, 1486–1500. [Google Scholar] [CrossRef] [Green Version]
- Altmeyer, M.; Neelsen, K.J.; Teloni, F.; Pozdnyakova, I.; Pellegrino, S.; Grøfte, M.; Rask, M.-B.D.; Streicher, W.; Jungmichel, S.; Nielsen, M.L.; et al. Liquid demixing of intrinsically disordered proteins is seeded by poly(ADP-ribose). Nat. Commun. 2015, 6, 8088. [Google Scholar] [CrossRef] [Green Version]
- Sukhanova, M.V.; Singatulina, A.S.; Pastré, D.; Lavrik, O.I. Fused in Sarcoma (FUS) in DNA Repair: Tango with Poly(ADP-ribose) Polymerase 1 and Compartmentalisation of Damaged DNA. Int. J. Mol. Sci. 2020, 21, 7020. [Google Scholar] [CrossRef]
- Delattre, O. Gene fusion with an ETS DNA-binding domain caused by chromosome translocation in human tumours. Nature 1992, 359, 162–165. [Google Scholar] [CrossRef] [PubMed]
- Paronetto, M.P.; Miñana, B.; Valcárcel, J. The Ewing Sarcoma Protein Regulates DNA Damage-Induced Alternative Splicing. Mol. Cell 2011, 43, 353–368. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Stewart, E.; Goshorn, R.; Bradley, C.; Griffiths, L.M.; Benavente, C.; Twarog, N.R.; Miller, G.M.; Caufield, W.; Freeman, B.B.; Bahrami, A.; et al. Targeting the DNA Repair Pathway in Ewing Sarcoma. Cell Rep. 2014, 9, 829–840. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Syed, A.; Tainer, J.A. The MRE11–RAD50–NBS1 Complex Conducts the Orchestration of Damage Signaling and Outcomes to Stress in DNA Replication and Repair. Annu. Rev. Biochem. 2018, 87, 263–294. [Google Scholar] [CrossRef] [PubMed]
- Daley, J.M.; Gaines, W.A.; Kwon, Y.; Sung, P. Regulation of DNA Pairing in Homologous Recombination. Cold Spring Harb. Perspect. Biol. 2014, 6, a017954. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Wu, D.; Topper, L.M.; Wilson, T.E. Recruitment and Dissociation of Nonhomologous End Joining Proteins at a DNA Double-Strand Break in Saccharomyces cerevisiae. Genetics 2008, 178, 1237–1249. [Google Scholar] [CrossRef]
- Pannunzio, N.R.; Watanabe, G.; Lieber, M.R. Nonhomologous DNA end-joining for repair of DNA double-strand breaks. J. Biol. Chem. 2018, 293, 10512–10523. [Google Scholar] [CrossRef] [Green Version]
- Davis, A.J.; Chen, D.J. DNA double strand break repair via non-homologous end-joining. Transl. Cancer Res. 2013, 2, 130–143. [Google Scholar] [CrossRef]
- Symington, L.S. Mechanism and regulation of DNA end resection in eukaryotes. Crit. Rev. Biochem. Mol. Biol. 2016, 51, 195–212. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Bonilla, B.; Hengel, S.R.; Grundy, M.K.; Bernstein, K.A. RAD51 Gene Family Structure and Function. Annu. Rev. Genet. 2020, 54, 25–46. [Google Scholar] [CrossRef]
- Agmon, N.; Liefshitz, B.; Zimmer, C.; Fabre, E.; Kupiec, M. Effect of nuclear architecture on the efficiency of double-strand break repair. Nat. Cell Biol. 2013, 15, 694–699. [Google Scholar] [CrossRef]
- Aylon, Y.; Liefshitz, B.; Bitan-Banin, G.; Kupiec, M. Molecular Dissection of Mitotic Recombination in the Yeast Saccharomyces cerevisiae. Mol. Cell. Biol. 2003, 23, 1403–1417. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Pascarella, G.; Hon, C.C.; Hashimoto, K.; Busch, A.; Luginbühl, J.; Parr, C.; Hin Yip, W.; Abe, K.; Kratz, A.; Bonetti, A.; et al. Recombination of repeat elements generates somatic complexity in human genomes. Cell 2022, 185, 3025–3040.e6. [Google Scholar] [CrossRef] [PubMed]
- Greene, E.C. DNA Sequence Alignment during Homologous Recombination. J. Biol. Chem. 2016, 291, 11572–11580. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Dutta, A.; Eckelmann, B.; Adhikari, S.; Ahmed, K.M.; Sengupta, S.; Pandey, A.; Hegde, P.M.; Tsai, M.-S.; Tainer, J.A.; Weinfeld, M.; et al. Microhomology-mediated end joining is activated in irradiated human cells due to phosphorylation-dependent formation of the XRCC1 repair complex. Nucleic Acids Res. 2016, 45, 2585–2599. [Google Scholar] [CrossRef] [Green Version]
- Simsek, D.; Furda, A.; Gao, Y.; Artus, J.; Brunet, E.; Hadjantonakis, A.-K.; Van Houten, B.; Shuman, S.; McKinnon, P.J.; Jasin, M. Crucial role for DNA ligase III in mitochondria but not in Xrcc1-dependent repair. Nature 2011, 471, 245–248. [Google Scholar] [CrossRef]
- Caracciolo, D.; Montesano, M.; Tagliaferri, P.; Tassone, P. Alternative non-homologous end joining repair: A master regulator of genomic instability in cancer. Precis. Cancer Med. 2019, 2, 8. [Google Scholar] [CrossRef]
- Anand, R.; Ranjha, L.; Cannavo, E.; Cejka, P. Phosphorylated CtIP Functions as a Co-factor of the MRE11-RAD50-NBS1 Endonuclease in DNA End Resection. Mol. Cell 2016, 64, 940–950. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Lisby, M.; Rothstein, R. Cell Biology of Mitotic Recombination. Cold Spring Harb. Perspect. Biol. 2015, 7, a016535. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Bekker-Jensen, S.; Lukas, C.; Kitagawa, R.; Melander, F.; Kastan, M.B.; Bartek, J.; Lukas, J. Spatial organization of the mammalian genome surveillance machinery in response to DNA strand breaks. J. Cell Biol. 2006, 173, 195–206. [Google Scholar] [CrossRef] [PubMed]
- Essers, J. Nuclear dynamics of RAD52 group homologous recombination proteins in response to DNA damage. EMBO J. 2002, 21, 2030–2037. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Lisby, M.; Barlow, J.H.; Burgess, R.C.; Rothstein, R. Choreography of the DNA Damage Response: Spatiotemporal Relationships among Checkpoint and Repair Proteins. Cell 2004, 118, 699–713. [Google Scholar] [CrossRef] [Green Version]
- Cruz, C.; Castroviejo-Bermejo, M.; Gutiérrez-Enríquez, S.; Llop-Guevara, A.; Ibrahim, Y.H.; Gris-Oliver, A.; Bonache, S.; Morancho, B.; Bruna, A.; Rueda, O.M.; et al. RAD51 foci as a functional biomarker of homologous recombination repair and PARP inhibitor resistance in germline BRCA-mutated breast cancer. Ann. Oncol. 2018, 29, 1203–1210. [Google Scholar] [CrossRef]
- Lisby, M.; Rothstein, R.; Mortensen, U.H. Rad52 forms DNA repair and recombination centers during S phase. Proc. Natl. Acad. Sci. USA 2001, 98, 8276–8282. [Google Scholar] [CrossRef] [Green Version]
- Altmannova, V.; Eckert-Boulet, N.; Arneric, M.; Kolesar, P.; Chaloupkova, R.; Damborsky, J.; Sung, P.; Zhao, X.; Lisby, M.; Krejci, L. Rad52 SUMOylation affects the efficiency of the DNA repair. Nucleic Acids Res. 2010, 38, 4708–4721. [Google Scholar] [CrossRef] [Green Version]
- Miné-Hattab, J.; Heltberg, M.; Villemeur, M.; Guedj, C.; Mora, T.; Walczak, A.M.; Dahan, M.; Taddei, A. Single molecule microscopy reveals key physical features of repair foci in living cells. eLife 2021, 10, e60577. [Google Scholar] [CrossRef]
- Hyman, A.A.; Weber, C.A.; Jülicher, F. Liquid-Liquid Phase Separation in Biology. Annu. Rev. Cell Dev. Biol. 2014, 30, 39–58. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Erdel, F.; Rippe, K. Formation of Chromatin Subcompartments by Phase Separation. Biophys. J. 2018, 114, 2262–2270. [Google Scholar] [CrossRef] [Green Version]
- Jost, D.; Vaillant, C.; Meister, P. Coupling 1D modifications and 3D nuclear organization: Data, models and function. Curr. Opin. Cell Biol. 2017, 44, 20–27. [Google Scholar] [CrossRef] [PubMed]
- Banani, S.F. Biomolecular condensates: Organizers of cellular biochemistry. Nat. Rev. Mol. Cell Biol. 2017, 18, 258–298. [Google Scholar] [CrossRef]
- McSwiggen, D.T.; Hansen, A.S.; Teves, S.S.; Marie-Nelly, H.; Hao, Y.; Heckert, A.B.; Umemoto, K.K.; Dugast-Darzacq, C.; Tjian, R.; Darzacq, X. Evidence for DNA-mediated nuclear compartmentalization distinct from phase separation. eLife 2019, 8, e47098. [Google Scholar] [CrossRef] [PubMed]
- Weber, S.C.; Brangwynne, C.P. Inverse Size Scaling of the Nucleolus by a Concentration-Dependent Phase Transition. Curr. Biol. 2015, 25, 641–646. [Google Scholar] [CrossRef] [Green Version]
- West, J.A.; Mito, M.; Kurosaka, S.; Takumi, T.; Tanegashima, C.; Chujo, T.; Yanaka, K.; Kingston, R.E.; Hirose, T.; Bond, C.; et al. Structural, super-resolution microscopy analysis of paraspeckle nuclear body organization. J. Cell Biol. 2016, 214, 817–830. [Google Scholar] [CrossRef] [Green Version]
- Weber, S.C. Evidence for and against Liquid-Liquid Phase Separation in the Nucleus. ncRNA 2019, 5, 50. [Google Scholar] [CrossRef] [Green Version]
- Oshidari, R.; Huang, R.; Medghalchi, M.; Tse, E.Y.W.; Ashgriz, N.; Lee, H.O.; Wyatt, H.; Mekhail, K. DNA repair by Rad52 liquid droplets. Nat. Commun. 2020, 11, 695. [Google Scholar] [CrossRef] [Green Version]
- Waterman, D.P.; Zhou, F.; Li, K.; Lee, C.-S.; Tsabar, M.; Eapen, V.V.; Mazzella, A.; Haber, J.E. Live cell monitoring of double strand breaks in S. cerevisiae. PLoS Genet. 2019, 15, e1008001. [Google Scholar] [CrossRef]
- Kilic, S.; Lezaja, A.; Gatti, M.; Bianco, E.; Michelena, J.; Imhof, R.; Altmeyer, M. Phase separation of 53 BP 1 determines liquid-like behavior of DNA repair compartments. EMBO J. 2019, 38, e101379. [Google Scholar] [CrossRef] [PubMed]
- Pessina, F.; Giavazzi, F.; Yin, Y.; Gioia, U.; Vitelli, V.; Galbiati, A.; Barozzi, S.; Garre, M.; Oldani, A.; Flaus, A.; et al. Functional transcription promoters at DNA double-strand breaks mediate RNA-driven phase separation of damage-response factors. Nat. Cell Biol. 2019, 21, 1286–1299. [Google Scholar] [CrossRef] [PubMed]
- Schrank, B.R.; Aparicio, T.; Li, Y.; Chang, W.; Chait, B.T.; Gundersen, G.G.; Gottesman, M.E.; Gautier, J. Nuclear Arp2/3 drives DNA break clustering for homology-directed repair. Nature 2018, 559, 61–66. [Google Scholar] [CrossRef] [PubMed]
- Sollazzo, A.; Brzozowska, B.; Cheng, L.; Lundholm, L.; Scherthan, H.; Wojcik, A. Live Dynamics of 53BP1 Foci Following Simultaneous Induction of Clustered and Dispersed DNA Damage in U2OS Cells. Int. J. Mol. Sci. 2018, 19, 519. [Google Scholar] [CrossRef] [Green Version]
- Manley, S.; Gillette, J.M.; Patterson, G.H.; Shroff, H.; Hess, H.F.; Betzig, E.; Lippincott-Schwartz, J. High-density mapping of single-molecule trajectories with photoactivated localization microscopy. Nat. Methods 2008, 5, 155–157. [Google Scholar] [CrossRef] [Green Version]
- Oswald, F.; Bank, E.L.M.; Bollen, Y.J.M.; Peterman, E.J.G. Imaging and quantification of trans-membrane protein diffusion in living bacteria. Phys. Chem. Chem. Phys. 2014, 16, 12625–12634. [Google Scholar] [CrossRef]
- Erdel, F.; Rademacher, A.; Vlijm, R.; Tünnermann, J.; Frank, L.; Weinmann, R.; Schweigert, E.; Yserentant, K.; Hummert, J.; Bauer, C.; et al. Mouse Heterochromatin Adopts Digital Compaction States without Showing Hallmarks of HP1-Driven Liquid-Liquid Phase Separation. Mol. Cell 2020, 78, 236–249.e7. [Google Scholar] [CrossRef]
- Heltberg, M.L.; Mine-Hattab, J.; Taddei, A.; Walczak, A.M.; Mora, T. Physical observables to determine the nature of membrane-less cellular sub-compartments. bioRxiv 2021. [Google Scholar] [CrossRef]
- Klosin, A.; Hyman, A.A. A liquid reservoir for silent chromatin. Nature 2017, 547, 168–169. [Google Scholar] [CrossRef] [Green Version]
- Larson, D.R.; Zenklusen, D.; Wu, B.; Chao, J.A.; Singer, R.H. Real-Time Observation of Transcription Initiation and Elongation on an Endogenous Yeast Gene. Science 2011, 332, 475–478. [Google Scholar] [CrossRef]
- Strom, A.R.; Emelyanov, A.V.; Mir, M.; Fyodorov, D.V.; Darzacq, X.; Karpen, G.H. Phase separation drives heterochromatin domain formation. Nature 2017, 547, 241–245. [Google Scholar] [CrossRef] [PubMed]
- Harami, G.M.; Kovács, Z.J.; Pancsa, R.; Pálinkás, J.; Baráth, V.; Tárnok, K.; Málnási-Csizmadia, A.; Kovács, M. Phase separation by ssDNA binding protein controlled via protein−protein and protein−DNA interactions. Proc. Natl. Acad. Sci. USA 2020, 117, 26206–26217. [Google Scholar] [CrossRef] [PubMed]
- Singatulina, A.S.; Hamon, L.; Sukhanova, M.V.; Desforges, B.; Joshi, V.; Bouhss, A.; Lavrik, O.I.; Pastré, D. PARP-1 Activation Directs FUS to DNA Damage Sites to Form PARG-Reversible Compartments Enriched in Damaged DNA. Cell Rep. 2019, 27, 1809–1821.e5. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Kroschwald, S.; Maharana, S.; Simon, A. Hexanediol: A chemical probe to investigate the material properties of membrane-less compartments. Matters 2017, 3, e201702000010. [Google Scholar] [CrossRef] [Green Version]
- Itoh, Y.; Iida, S.; Tamura, S.; Nagashima, R.; Shiraki, K.; Goto, T.; Hibino, K.; Ide, S.; Maeshima, K. 1,6-hexanediol rapidly immobilizes and condenses chromatin in living human cells. Life Sci. Alliance 2021, 4, e202001005. [Google Scholar] [CrossRef]
- Düster, R.; Kaltheuner, I.H.; Schmitz, M.; Geyer, M. 1,6-Hexanediol, commonly used to dissolve liquid–liquid phase separated condensates, directly impairs kinase and phosphatase activities. J. Biol. Chem. 2021, 296, 100260. [Google Scholar] [CrossRef]
- Irgen-Gioro, S.; Walling, V.; Chong, S. Fixation Can Change the Appearance of Phase Separation in Living Cells. bioRxiv 2022. [Google Scholar] [CrossRef]
- Ray Chaudhuri, A.; Nussenzweig, A. The multifaceted roles of PARP1 in DNA repair and chromatin remodelling. Nat. Rev. Mol. Cell Biol. 2017, 18, 610–621. [Google Scholar] [CrossRef]
- Lesterlin, C.; Ball, G.; Schermelleh, L.; Sherratt, D.J. RecA bundles mediate homology pairing between distant sisters during DNA break repair. Nature 2014, 506, 249–253. [Google Scholar] [CrossRef] [Green Version]
- Wiktor, J.; Gynnå, A.H.; Leroy, P.; Larsson, J.; Coceano, G.; Testa, I.; Elf, J. RecA finds homologous DNA by reduced dimensionality search. Nature 2021, 597, 426–429. [Google Scholar] [CrossRef]
- Ochs, F.; Karemore, G.; Miron, E.; Brown, J.; Sedlackova, H.; Rask, M.-B.; Lampe, M.; Buckle, V.; Schermelleh, L.; Lukas, J.; et al. Stabilization of chromatin topology safeguards genome integrity. Nature 2019, 574, 571–574. [Google Scholar] [CrossRef] [PubMed]
- Chapman, J.R.; Sossick, A.J.; Boulton, S.J.; Jackson, S.P. BRCA1-associated exclusion of 53BP1 from DNA damage sites underlies temporal control of DNA repair. J. Cell Sci. 2012, 125, 3529–3534. [Google Scholar] [CrossRef] [Green Version]
- Reindl, J.; Girst, S.; Walsh, D.W.M.; Greubel, C.; Schwarz, B.; Siebenwirth, C.; Drexler, G.A.; Friedl, A.A.; Dollinger, G. Chromatin organization revealed by nanostructure of irradiation induced γH2AX, 53BP1 and Rad51 foci. Sci. Rep. 2017, 7, 40616. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Zarebski, M.; Wiernasz, E.; Dobrucki, J.W. Recruitment of heterochromatin protein 1 to DNA repair sites. Cytometry 2009, 75A, 619–625. [Google Scholar] [CrossRef] [PubMed]
- Kordon, M.M.; Zarębski, M.; Solarczyk, K.; Ma, H.; Pederson, T.; Dobrucki, J.W. STRIDE—A fluorescence method for direct, specific in situ detection of individual single- or double-strand DNA breaks in fixed cells. Nucleic Acids Res. 2020, 48, e14. [Google Scholar] [CrossRef]
- Protter, D.S.W.; Rao, B.S.; Van Treeck, B.; Lin, Y.; Mizoue, L.; Rosen, M.K.; Parker, R. Intrinsically Disordered Regions Can Contribute Promiscuous Interactions to RNP Granule Assembly. Cell Rep. 2018, 22, 1401–1412. [Google Scholar] [CrossRef] [Green Version]
- Molliex, A.; Temirov, J.; Lee, J.; Coughlin, M.; Kanagaraj, A.P.; Kim, H.J.; Mittag, T.; Taylor, J.P. Phase Separation by Low Complexity Domains Promotes Stress Granule Assembly and Drives Pathological Fibrillization. Cell 2015, 163, 123–133. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Cascarina, S.M.; Elder, M.R.; Ross, E.D. Atypical structural tendencies among low-complexity domains in the Protein Data Bank proteome. PLoS Comput. Biol. 2020, 16, e1007487. [Google Scholar] [CrossRef] [Green Version]
- Luo, Y.; Na, Z.; Slavoff, S.A. P-Bodies: Composition, Properties, and Functions. Biochemistry 2018, 57, 2424–2431. [Google Scholar] [CrossRef] [Green Version]
- Campos-Melo, D.; Hawley, Z.C.E.; Droppelmann, C.A.; Strong, M.J. The Integral Role of RNA in Stress Granule Formation and Function. Front. Cell Dev. Biol. 2021, 9, 621779. [Google Scholar] [CrossRef]
- Leung, A.K.L. Poly(ADP-ribose): A Dynamic Trigger for Biomolecular Condensate Formation. Trends Cell Biol. 2020, 30, 370–383. [Google Scholar] [CrossRef]
- Shin, Y.; Chang, Y.-C.; Lee, D.S.W.; Berry, J.; Sanders, D.W.; Ronceray, P.; Wingreen, N.S.; Haataja, M.; Brangwynne, C.P. Liquid Nuclear Condensates Mechanically Sense and Restructure the Genome. Cell 2018, 175, 1481–1491.e13. [Google Scholar] [CrossRef] [Green Version]
- Poudyal, R.R.; Pir Cakmak, F.; Keating, C.D.; Bevilacqua, P.C. Physical Principles and Extant Biology Reveal Roles for RNA-Containing Membraneless Compartments in Origins of Life Chemistry. Biochemistry 2018, 57, 2509–2519. [Google Scholar] [CrossRef]
- Alberti, S.; Gladfelter, A.; Mittag, T. Considerations and Challenges in Studying Liquid-Liquid Phase Separation and Biomolecular Condensates. Cell 2019, 176, 419–434. [Google Scholar] [CrossRef] [Green Version]
- Igelmann, S.; Lessard, F.; Ferbeyre, G. Liquid–Liquid Phase Separation in Cancer Signaling, Metabolism and Anticancer Therapy. Cancers 2022, 14, 1830. [Google Scholar] [CrossRef] [PubMed]
- Lu, J.; Qian, J.; Xu, Z.; Yin, S.; Zhou, L.; Zheng, S.; Zhang, W. Emerging Roles of Liquid–Liquid Phase Separation in Cancer: From Protein Aggregation to Immune-Associated Signaling. Front. Cell Dev. Biol. 2021, 9, 631486. [Google Scholar] [CrossRef]
Proteins | Organisms | Physical Nature of the Condensate | Sphericity | Fusion | Internal Dynamics | Diffusion across Boundary | Concentration Dependence |
---|---|---|---|---|---|---|---|
SSB | E. coli | LLPS | - | - | Yes (FRAP in vitro) [62] | - | Yes in vitro [62] |
RPA1 | S.c yeast | Not LLPS | - | - | No (Identical to chromatin) [40] | No [40] | - |
Rad52 | S.c yeast | LLPS | Yes [49] | Yes [40,49] | Yes [40] | Yes [40] | No [40] |
PARP-1 | Human | Initiate only LLPS | - | - | - | - | - |
FUS | Human | LLPS | Yes [12,67] | Yes [12] | - | - | - |
EWS | Human | LLPS | Yes [12,67] | Yes [12] | - | - | - |
TAF15 | Human | LLPS | Yes [12,67] | Yes [12] | - | - | - |
53BP1 | Human | LLPS | Yes [12] | Yes [12] | - | - | - |
p53 | Human | Client of LLPS [51] | - | - | - | - | - |
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Miné-Hattab, J.; Liu, S.; Taddei, A. Repair Foci as Liquid Phase Separation: Evidence and Limitations. Genes 2022, 13, 1846. https://doi.org/10.3390/genes13101846
Miné-Hattab J, Liu S, Taddei A. Repair Foci as Liquid Phase Separation: Evidence and Limitations. Genes. 2022; 13(10):1846. https://doi.org/10.3390/genes13101846
Chicago/Turabian StyleMiné-Hattab, Judith, Siyu Liu, and Angela Taddei. 2022. "Repair Foci as Liquid Phase Separation: Evidence and Limitations" Genes 13, no. 10: 1846. https://doi.org/10.3390/genes13101846